I’m able to add an entry to .classpath using just the eclipse plugin, but this doesn’t seem to work when the project is imported with Buildship 1.0.12. I stumbled across the linked topic from about a year ago and was wondering if there had been any progress made towards allowing customization of the .classpath/.project files?

I figured out that BuildShip only imports projects and while that works up to a point, how will users be able to customize the project files built? As an example, I need to change the project output directory, add additional natures to the .project file and additional containers to the .classpath file. Will BS be updated to read the eclipse closure in the build.gradle or are there other mechanisms on the horizon?

What kind of entries are you referring to? Buildship already handles project and external dependencies as well as source folders.

To make Buildship aware of other adjustments, we first need to replace the XML-manipulation-based approach in Gradle Core with a model-based approach. This is something we want to do, but there is no concrete plan as to when.